[maker-devel] Repeat masking in Maker

[Muriel Gros-Balthazard]

Hello,

I generated my own library of repeats following the tutorial provided 
with Maker.
I also wanted to use all the species from the RepBase library for the 
masking.

It is not clear to me how this works in Maker.
Indeed, I put both these options :
model_org=all
rmlib=allRepeats.lib

However, when using RepeatMasker without Maker, you can't put both -lib 
allRepeats.lib and -species all as options.
Indeed, you can only say one species when also using the -lib option 
(-species arabidopsis for instance and not -species all)

What about Maker ?

Do I have masking of allRepeats.lib and also of all species repeats if I 
put these two arguments in Maker ?
model_org=all
rmlib=allRepeats.lib

Another question:
It is said that RepeatRunner is used as well. I put the option: 
repeat_protein=te_proteins.fasta
But realized that RepeatRunner was not installed on my computer !!!
I had no problem to run Maker.
So, this file of te_proteins is used rather by RepeatMasker to mask them ?
It is not clear to me how RepeatRunner is involved in the pipeline ?

Thanks a lot for your answers,

Muriel

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